My Father in law has a 2006 Ford f250 and a 2004 cougar 5th wheel. He has had some problems with his brake controller/ brakes not working. He can take a 10 hour trip each way with no problems but then...
My first suspect would be wiring. I know that I can lose communication intermittently if that plug isn't firmly seated. I'd clean the prongs on the plug, not too much you can do on the female side tho.